Add --flow-rate-factor option

[johannesring]

This change adds a compute_flow_rate function and a --flow-rate-factor option to fsipy-mesh. The default value is 0.31. The function is copied more or less from VaMPy and maybe this change should be added in VaMPy instead.

[keiyamamo]

@johannesring - Looks nice! Out of curiosity, where does 0.31 come from ?
@hkjeldsberg - Is this something that might be useful in VaMPy? If so, I think it should go to VaMPy instead.

[hkjeldsberg]

@keiyamamo this could definitely be useful in VaMPy too. Regarding the value 0.31 I can see that it is currently set to 0.27 in Vampy, but the source of either of these values are vague. I think one or both of them stem from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943236/pdf/nihms232282.pdf – See Table 1, VFR_avg for ICA. I could be wrong though. KVS´paper also uses this value (245 ml/min): https://link.springer.com/article/10.1007/s10439-015-1288-5
So I think this value (245) somehow translates into one of the above.

[johannesring]

@keiyamamo - 0.31 is what we have been using in our simulations. @KristianValen-Sendstad can elaborate.
@hkjeldsberg - Ok, I will make a pull request in VaMPy.

[keiyamamo]

@johannesring @hkjeldsberg Thank you for the explanation!

[KristianValen-Sendstad]

Yes, Kei. You are absolutely right. After a rather tedious process of finding the "correct" (well, least wrong :) flow rates, we concluded that .31m/s should be the correct velocity to impose on all ICAs in the Aneurisk Database. Later though, we were a little more cautious since we were assessing "turbulence" in the ICA and adjusted the value down to .27m/s. These numbers are so close that it doesn't really matter what we use, but I think .31m/s is more correct. KVS

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On Thu, 31 Aug 2023 at 14:28, Kei Yamamoto ***@***.***> wrote: @johannesring <https://github.com/johannesring> @hkjeldsberg <https://github.com/hkjeldsberg> Thank you for the explanation! — Reply to this email directly, view it on GitHub <#35 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA4X54MJ5IPA7EBLRNKFNFLXYB7O7ANCNFSM6AAAAAA4EGK3WU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[keiyamamo]

@KristianValen-Sendstad Thank you for the detailed explanation!

[johannesring]

I have removed the compute_flow_rate function and reverted back to use the one in VaMPY instead. This requires the latest VaMPY from the master branch to work. The --flow-rate-factor is still needed in our code and the default flow rate factor is set to 0.31,

[johannesring]

I see that the test fails because it uses VaMPY from before pull request #120 was merged. It looks like this is because the conda environment is cached and I will try to figure out how to clear the cache.

[johannesring]

I restarted the failing jobs and now they are all green (I didn't have to clear the cache), so I am merging this now.